CHARACTERIZING THE STRUCTURE AND DYNAMICS OF ADAPTIVE IMMUNE PROTEINS TO INFORM IMMUNOTHERAPY DESIGN
Degree type
Graduate group
Discipline
Immunology and Infectious Disease
Biochemistry, Biophysics, and Structural Biology
Subject
interleukin-2
major histocompatability complex
MHC
Nuclear Magnetic Resonance
T cell receptor
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Abstract
Human interleukin-2 (IL-2) is a crucial cytokine for T cell regulation, with therapeutic potential in cancer and autoimmune diseases. However, IL-2's pleiotropic effects across different immune cell types often lead to toxicity and limited efficacy. The first study in this thesis presents a detailed characterization of IL-2 dynamics compared to two engineered IL-2 mutants, “superkines” S15 and S1, which exhibit biased signaling towards effector T cells. Using NMR spectroscopy and molecular dynamics simulations, we demonstrate significant variations in core dynamic landscapes across the three variants. Furthermore, we rationally design a mutation (L56A) in the S1 core network, which partially reverts its dynamics, receptor binding affinity, and T cell signaling behavior. Our results suggest that modulating IL-2 dynamics is an untapped approach for designing immunotherapies with improved immune cell selectivity profiles.The intrinsic instability and inconsistent T cell receptor binding mode of the class I major histocompatibility complex (MHC-I) are fundamental challenges that hinder development of therapeutics. The second study leverages the positive allosteric coupling between the peptide and β2m subunits of MHC-I by engineering a disulfide bond bridging conserved epitopes across the HC/β2m interface to generate stable, peptide-receptive molecules. Using solution NMR, we demonstrate that the disulfide bond induces long-range conformational and dynamical changes in the α2-1 helix., indicating that the interchain disulfide bond stabilizes MHC-I molecules in an open conformation to promote peptide exchange. In the third study, we demonstrate the application of a designed MHC-I design, SMART A02:01, for solution mapping of the A6c134 TCR docking footprint using NMR spectroscopy. We establish that the use of our engineered construct recapitulates the native conformation of the MHC-I peptide binding groove and accurately detects the critical binding sites on SMART A02:01 that engage A6c134. Our approach allows for high-resolution mapping of TCR/MHC-I interactions, alleviating the need for complete structure elucidation, and may be paired with computational modeling approaches for structure-guided optimization and clinical development. Taken together, solution NMR techniques provide high-resolution insights into protein structure and conformational dynamics. Furthermore, these efforts highlight the application of NMR analyses to inform rational protein design and guide the development of diagnostics and therapeutics.